In this paper, a robust fault tolerant control reconfiguration is proposed. For identified models whose parameters change according to operating conditions, it is convenient to design a reconfiguration control strategy. This approach switches on-line the right controller to achieve the same performances for a given objective. This reconfiguration strategy is based on robust flatness-based switching control and developed in discrete-time framework in order to track a reference trajectory starting from a flat output variable. For each model, a corresponding flatness-based controller is designed and consequently, a multi-controller structure is obtained. The switching process is based on the minimization of a criterion. The performances obtained by switching in terms of tracking trajectory and disturbance fault rejection are discussed in this paper. The stability of the corresponding switched discrete-time linear systems is given.